def make_berry_parser():
import re
from pwproc.util import parser_one_line
def parse_vector(vec, *, num_re=re.compile(r"-?[.\d]+")):
return tuple(map(float, num_re.findall(vec)))
gdir_re = re.compile(r"^[ \w]* direction of vector ([123])$")
phase_re = re.compile(r"^ +TOTAL PHASE: +(-?[.\d]+) \(mod (1|2)\)$")
vec_re = re.compile(r"^ +The polarization direction is: +\(( *(?:-?[.\d]+[ ,]*){3})\)$")
pol_re = re.compile(r"^ +P = +(-?[.\d]+) +\(mod +([.\d]+)\) +C/m\^2$")
g_parser = parser_one_line(gdir_re, lambda m: int(m.group(1)))
phase_parser = parser_one_line(phase_re, lambda m: (float(m.group(1)), int(m.group(2))))
vec_parser = parser_one_line(vec_re, lambda m: parse_vector(m.group(1)))
pol_parser = parser_one_line(pol_re, lambda m: tuple(map(float, m.group(1, 2))))
def berry_parser(f_name):
# type: (Path) -> Polarization
with open(f_name) as f:
gdir = g_parser(f)
f.seek(0)
phase = phase_parser(f)
f.seek(0)
vec = vec_parser(f)
f.seek(0)
pol = pol_parser(f)
return Polarization(gdir, phase, vec, pol)
return berry_parser
def get_init_basis(path):
# type: (Path) -> Tuple[float, Basis]
"""Extracts the initial basis in angstrom from pw.x output."""
from scipy import constants
from pwproc.util import parser_one_line, parser_with_header
bohr_to_ang = constants.value('Bohr radius') / constants.angstrom
alat_re = re.compile(
r"[ \t]+lattice parameter \(alat\)[ \t]+=[ \t]+([\d.]+)[ \t]+a\.u\.")
basis_head_re = re.compile(
r"[ \t]+crystal axes: \(cart. coord. in units of alat\)")
basis_line_re = re.compile(
r"[ \t]+a\([\d]\) = \(((?:[ \t]+[-.\d]+){3}[ \t]+)\)")
alat_parser = parser_one_line(alat_re, lambda m: float(m.group(1)))
basis_parser = parser_with_header(basis_head_re, basis_line_re,
lambda m: parse_vector(m.group(1)))
with open(path) as f:
alat: float = alat_parser(f)
# TODO: Remove seek and run parsers in correct order
f.seek(0)
basis = basis_parser(f)
# Convert basis from alat to angstrom
assert len(basis) == 3
basis = Basis(np.array(basis))
basis *= alat * bohr_to_ang
return alat, basis
def get_scf_energy(path):
# type: (str) -> float
"""Get the energy in Ry from pw.x output."""
import re
from pwproc.util import parser_one_line
energy_re = re.compile(r"![\s]+total energy[\s]+=[\s]+(-[\d.]+) Ry")
energy_parser = parser_one_line(energy_re, lambda m: float(m.group(1)))
with open(path) as f:
return energy_parser(f)
def find_fermi(path):
# type: (Path) -> Iterable[float]
"""Extract all records of the Fermi energy from pw.x output."""
import re
from pwproc.util import parser_one_line
fermi_re = re.compile(r"[ \t]+the Fermi energy is[ \t]+(-?[.\d]+) ev")
fermi_parser = parser_one_line(fermi_re,
lambda m: float(m.group(1)),
find_multiple=True)
with open(path) as f:
fe = fermi_parser(f)
return fe
def get_save_file(path):
# type: (Path) -> str
"""Extract the prefix from pw.x output."""
from pwproc.util import parser_one_line
save_re = re.compile(
r"^[ \t]+Writing output data file (?:\./)?([-.\w]+).save/?$")
save_parser = parser_one_line(save_re, lambda m: m.group(1))
with open(path) as f:
prefix = save_parser(f)
if prefix is None:
raise ParserError("Could not find calculation prefix")
return prefix